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(-) Description

Title :  STRUCTURE OF PLASMODIUM FALCIPARUM DXR IN COMPLEX WITH A BETA-SUBSTITUTED FOSMIDOMYCIN ANALOGUE, LC51 AND MANGANESE
 
Authors :  S. Sooriyaarachchi, T. Bergfors, T. A. Jones, S. L. Mowbray
Date :  12 Apr 16  (Deposition) - 24 Aug 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme-Inhibitor Complex, Mep Pathway, Isoprenoid Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sooriyaarachchi, R. Chofor, M. D. Risseeuw, T. Bergfors, J. Pouyez C. S. Dowd, L. Maes, J. Wouters, T. A. Jones, S. Van Calenbergh, S. L. Mowbray
Targeting An Aromatic Hotspot In Plasmodium Falciparum 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase With Beta-Arylpropyl Analogues Of Fosmidomycin.
Chemmedchem V. 11 2024 2016
PubMed-ID: 27487410  |  Reference-DOI: 10.1002/CMDC.201600249
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, APICOPLASTIC
    Chains: A, B
    EC Number: 1.1.1.267
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PEXP5-CT/TOPO
    Expression System Taxid: 469008
    Expression System Variant: C43
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 75-488
    Gene: DXR, PF14_0641
    Organ: APICOPLAST
    Organism Scientific: PLASMODIUM FALCIPARUM (ISOLATE 3D7)
    Organism Taxid: 36329
    Other Details: MATURE PROTEIN LACKS SIGNAL AND APICOPLAST TARGETING SEQUENCES
    Synonym: DXP REDUCTOISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
2GOL5Ligand/IonGLYCEROL
3LC52Ligand/Ion[(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-(NAPHTHALEN-1-YL)PENTYL]PHOSPHONIC ACID
4MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:205 , ASP A:231 , SER A:232 , GLU A:233 , SER A:269 , SER A:270 , MET A:298 , SER A:306 , ASN A:311 , LYS A:312 , GLU A:315 , HIS A:341 , ASP A:359 , MN A:502 , GOL A:503 , HOH A:602 , HOH A:610 , HOH A:626binding site for residue LC5 A 501
02AC2SOFTWARELYS A:205 , ASP A:231 , GLU A:233 , GLU A:315 , LC5 A:501binding site for residue MN A 502
03AC3SOFTWARESER A:232 , GLU A:233 , CYS A:268 , SER A:269 , SER A:270 , HIS A:335 , CYS A:338 , ILE A:340 , HIS A:341 , LC5 A:501binding site for residue GOL A 503
04AC4SOFTWARETYR A:113 , HIS A:136 , ILE A:181 , GLN A:185binding site for residue GOL A 504
05AC5SOFTWAREGLN A:239 , CYS A:240 , LEU A:241 , HOH A:612 , HOH A:625 , HOH A:632 , GLN B:239 , LEU B:241binding site for residue FMT A 505
06AC6SOFTWARELYS B:205 , ASP B:231 , SER B:232 , GLU B:233 , SER B:269 , SER B:270 , MET B:298 , SER B:306 , ASN B:311 , LYS B:312 , GLU B:315 , HIS B:341 , ASP B:359 , MET B:360 , MN B:502 , GOL B:503 , HOH B:602 , HOH B:614 , HOH B:620binding site for residue LC5 B 501
07AC7SOFTWARELYS B:205 , ASP B:231 , GLU B:233 , GLU B:315 , LC5 B:501binding site for residue MN B 502
08AC8SOFTWARESER B:232 , GLU B:233 , CYS B:268 , SER B:269 , SER B:270 , HIS B:335 , CYS B:338 , ILE B:340 , HIS B:341 , LC5 B:501binding site for residue GOL B 503
09AC9SOFTWARELYS B:223 , LYS B:226 , LEU B:247 , THR B:249 , GLN B:253 , ASN B:284 , ASN B:289 , HOH B:619 , HOH B:646 , HOH B:695binding site for residue GOL B 504
10AD1SOFTWAREVAL B:114 , ASN B:115 , HIS B:136binding site for residue GOL B 505
11AD2SOFTWARESER B:257 , ILE B:262 , ASP B:326 , ASP B:329binding site for residue FMT B 506
12AD3SOFTWAREVAL B:209 , SER B:210 , ASN B:413 , PHE B:414 , PRO B:416 , THR B:417 , HOH B:603binding site for residue FMT B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JAZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:370 -Pro A:371
2Trp B:370 -Pro B:371

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JAZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JAZ)

(-) Exons   (0, 0)

(no "Exon" information available for 5JAZ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.......eeeehhhhhhhhhhh....eeee...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhhh.......hhhhhh.eeeeeeee........hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jaz A  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHN 486
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486


Chain B from PDB  Type:PROTEIN  Length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.......eeeehhhhhhhhhhh....eeee...hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.hhhhhh.......hhhhhh.eeeeeeee........hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jaz B  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHN 486
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JAZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JAZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JAZ)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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        DXR_PLAF7 | Q8IKG4: 4y67 4y6p 4y6r 4y6s 5jbi 5jc1 5jmp 5jmw 5jnl 5jo0

(-) Related Entries Specified in the PDB File

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